Well, one antagonist could be Sasuke. If he goes down a dark path again, his actions could cause Naruto great pain. Minato would then watch as Naruto tries to deal with his best friend's betrayal or attacks. Zetsu is also a potential antagonist. He has his own hidden agendas and could be manipulating events behind the scenes to make Naruto suffer. And there are always the hidden threats within the shinobi world, like certain hidden village leaders who might see Naruto as a threat and try to harm him, with Minato observing all this.
One possible theme could be regret. Minato might feel regret for not being there to protect Naruto, which adds to the emotional turmoil as he watches his son suffer. Another theme could be the cycle of pain. Naruto's suffering might be seen as part of a larger cycle that Minato was unable to break. Also, there could be a theme of growth through adversity. Even though Minato is just watching, Naruto's suffering could lead to his growth as a character, and Minato might witness this transformation.
The Akatsuki could still be the main antagonists. However, in this fanfiction, they might target Naruto earlier because they know Minato is training him. They could fear that Naruto would become an even greater threat to their plans in the future. Pain, in particular, might see Naruto as a symbol of the Hidden Leaf's strength that needs to be eliminated. Also, there could be an internal antagonist within the Hidden Leaf, someone who is jealous of Naruto's special relationship with Minato and tries to undermine him.
The Akatsuki could still be the main antagonists. Even with Naruto being trained by Minato and becoming godlike, the Akatsuki's goals of collecting the tailed beasts would put them in direct conflict with Naruto. Their powerful members, like Pain or Itachi, would pose a great challenge to Naruto, despite his new skills.
It could be Orochimaru. He might be interested in the baby's unique genetic makeup, thinking he can use it to create more powerful experiments. He has always been obsessed with power and the baby's combination of Naruto and Temari's abilities would be very appealing to him.
The village elders could be the antagonists. They might have a hidden agenda and want Naruto out of the picture, so they imprison him unjustly.
Madara Uchiha could also be a possible antagonist in this scenario. Even if he is dead in the original story, in a fanfiction, his lingering influence or a resurrected form could manipulate Naruto. Madara was always against Konoha's ideals to some extent and might use Naruto as a tool to destroy what he hated.
One possible antagonist could be some of the traditionalist shinobi in the village who oppose Naruto's new family situation. They might see Kunou as a threat due to her heritage.
The Sound Ninjas could be great antagonists. They could use their own unique parkour - like skills to try and stop Naruto. They might be chasing him through the forest, and Naruto has to use his parkour skills to outmaneuver them.
The antagonists could be a secret organization within the Hidden Leaf Village itself. They are afraid that if Kurama is freed, it will bring destruction to the village. They think Naruto is being reckless and they will do anything to stop him, including framing him for crimes he didn't commit and turning his friends against him, all in an effort to keep Kurama sealed.
A group of rogue ninjas who have made the island their base could be antagonists. They might see Naruto as a threat to their operations on the island.